I ran though this and the timer (at least for now) is completely pointless. If you die it resets your timer and your progress, except it does not actually reset your weapons, skills, or crafted items it just resets the quests/outposts.

I actually made it through without dying and resetting and I still had around 30 min left on the timer. It adds time for pretty much everything that you do from getting a clean kill on an animal to completing quests.

Yeah, watch the timer closely ... if you capture it w/o any alarms or being detected, you will get awarded 5:00 3 times, and then the game takes away 5:00 2 times, leaving you with a single 5:00 bonus.